HABITAT USE BY BOTTLENOSE DOLPHINS IN THE INDIAN RIVER LAGOON by Rachael M. Greller A Thesis Submitted to the Faculty of Charles E. Schmidt College of Science In Partial Fulfilment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL May 2019 Copyright 2019 by Rachael M. Greller ii HABITAT USE BY BOTTLENOSE DOLPHINS IN THE INDIAN RIVER LAGOON by Rachael M. Greller This thesis was prepared under the direction of the candidate's thesis advisor, Dr. Scott Markwith, Department of Geosciences, and has been approved by all members of the supervisory committee. It was submitted to the faculty of the Charles E. Schmidt College of Science and was accepted in partial fulfillment of the requirements for the degree of Master of Science. CO:rvnvtiTTEE: cott Markwith, Ph.D. Thesis Advisor Weibo Liu, Ph.D. Zhixiao Xie, Ph.D. Chair, Geosciences ~::::::hmidt College of Science Khaled Sob han, Ph.D. Interim Dean, Graduate College 111 ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Scott Markwith for his support and guidance during my graduate college experience. I’d also like to thank Harbor Branch Oceanographic Institute (HBOI) for their data collection and funding of my thesis, along with the Fisheries Independent Monitoring (FIM) Program a part of the Florida Fish and Wildlife Conservation Commission. A special thanks to Richard Paperno for his hard work collecting the FIM data and to Brandy Nelson from HBOI who encouraged me along the way. I would finally like to thank my fellow graduate students in the department who supported me. iv ABSTRACT Author: Rachael M. Greller Title: Habitat Use By Bottlenose Dolphins In The Indian River Lagoon Institution: Florida Atlantic University Thesis Advisor: Dr. Scott Markwith Degree: Master of Science Year: 2019 The objective of this research was to examine bottlenose dolphin (Tursiops truncatus) habitat use in the Indian River Lagoon (IRL) based on monthly relocation of photo- identified individuals, prey availability and environmental factors from 2003-2015. We focused on the variation of spatial and temporal abiotic and biotic factors and their influence on bottlenose dolphin habitat use patterns. Harbor Branch Oceanographic Institute (HBOI) conducted monthly photo-identification surveys along the length of the IRL and GPS locations of photographed dolphins were collected at the time of surveying. Stratified random samples of prey and environmental variables were collected monthly by the Florida Fish and Wildlife Conservation Commission (FWC) as part of the Fisheries-Independent Monitoring (FIM) program. Kernel density estimation was used to determine the magnitude-per-unit area of dolphins across a continuous raster surface of the IRL by wet and dry seasons each year, the values of which were used as a response variable in Classification and regression tree (CART) analyses with FIM fish community v and environmental factors as predictors. Understanding how dolphins respond to environmental factors over time in the IRL could be used to predict future responses in estuaries and prioritize conservation and restoration actions. vi HABITAT USE BY BOTTLENOSE DOLPHINS IN THE INDIAN RIVER LAGOON LIST OF TABLES ............................................................................................................. ix LIST OF FIGURES ............................................................................................................ x INTRODUCTION .............................................................................................................. 1 Background ................................................................................................................... 1 Objective ....................................................................................................................... 3 METHODS ......................................................................................................................... 5 Study Area .................................................................................................................... 5 Species Description ...................................................................................................... 7 Data Collection ........................................................................................................... 11 ANALYSIS ...................................................................................................................... 16 Kernel Density Estimation .......................................................................................... 16 Non-metric Multidimensional Scaling ....................................................................... 17 Classification and Regression Tree ............................................................................ 18 RESULTS ......................................................................................................................... 22 Kernel Density Estimation .......................................................................................... 22 Non-metric Multidimensional Scaling ....................................................................... 37 Classification and Regression Tree ............................................................................ 38 DISCUSSION ................................................................................................................... 43 CONCLUSION ................................................................................................................ 48 vii REFERENCES ................................................................................................................. 49 viii LIST OF TABLES Table 1. Number of observations for each year and season of dolphin sampling data ..... 12 Table 2. Description of monthly monitoring sampling gears used for each sampling period. Table FIM16-01 (FWC-FWRI, 2014) ............................................................ 14 Table 3. Model variables used in the CART analyses ...................................................... 20 Table 4. Mean salinity and standard deviation for each section, season, and year in the IRL ........................................................................................................................ 31 Table 5. SR mean and standard deviation for each section, season, and year in the IRL .............................................................................................................................. 33 Table 6. DO mean and standard deviation for each section, season, and year in the IRL .............................................................................................................................. 35 Table 7. Water temperature mean and standard deviation for each section, season, and year in the IRL ..................................................................................................... 36 Table 8. NMS fish species with scientific and common name, and corresponding correlation coefficient (r) ............................................................................................ 37 Table 9. Bottom type codes (FWC-FWRI, 2014) ............................................................. 38 Table 10. Shore type codes (FWC-FWRI, 2014) ............................................................. 39 ix LIST OF FIGURES Figure 1. The IRL sub-divided into six segments based on hydrodynamics and geographic features (Mazzoil, et al.2008). .................................................................... 6 Figure 2. Bottlenose dolphin (Tursiops truncatus) (photo: Bushak, 2013) ......................... 8 Figure 3. Map of the Indian River Lagoon (IRL), Florida showing core areas for each community, calculated using a 50% fixed kernel density home range for each individual (Titcomb et.al, 2015). ................................................................................... 9 Figure 4. Food web for bottlenose dolphins and their prey in the IRL (Barros & Wells, 1998) ................................................................................................................ 11 Figure 5. Dry season Schoener’s D and I statistics comparing each sampling year from 2003-2015 to the mean KDE surface ................................................................. 23 Figure 6. Wet season Schoener’s D and I statistics comparing each sampling year from 2003-2015 to the mean KDE surface ................................................................. 23 Figure 7. Dry season KDE maps for 2003-2006 .............................................................. 25 Figure 8. Dry season KDE maps for 2007-2011 ............................................................... 26 Figure 9. Dry season KDE maps for 2012-2015 ............................................................... 27 Figure 10. Wet season KDE maps for 2003-2006 ............................................................ 28 Figure 11. Wet season KDE maps for 2007-2011 ............................................................ 29 Figure 12. Wet season KDE maps for 2012-2015 ............................................................ 30 Figure 13. The figure shows the mean salinity over the dry season for each year and section in the IRL ........................................................................................................ 32 x Figure 14. The figure shows the mean salinity over the wet season for each year and section in the IRL .......................................................................................................